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authorB. Watson <yalhcru@gmail.com>2022-03-12 14:40:15 -0500
committerB. Watson <yalhcru@gmail.com>2022-03-12 14:40:15 -0500
commit4d4223562bfeb7d8aba7115b9a03c7f0d490910c (patch)
treed9dcbffa279287824daf524b73833d255db54291 /academic
parent3ee347b33c9f8673b90f44d4e02006912ed7335d (diff)
academic/treebest-ensembl: Wrap README at 72 columns.
Signed-off-by: B. Watson <yalhcru@gmail.com>
Diffstat (limited to 'academic')
-rw-r--r--academic/treebest-ensembl/README12
1 files changed, 7 insertions, 5 deletions
diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README
index b6639d304d23..f91a651be9ee 100644
--- a/academic/treebest-ensembl/README
+++ b/academic/treebest-ensembl/README
@@ -10,16 +10,18 @@ TreeBeST is previously known as NJTREE. It has been largely used in the
TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting
group.
-This is the Ensembl Compara modifications version. The main new features
-are:
+This is the Ensembl Compara modifications version. The main new
+features are:
1) -s option in treebest sdi, to allow a user-defined species tree.
T node-tag in the NHX output: a bit-field listing the input trees
2) that support the node.
3) -I option in treebest nj, to carry on the T tags from the input tree
-4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK
-5) -X option in treebest best, to give a higher weight to the likelihood
- that comes from the reconciliation with the species tree (default 1)
+4) -Z option in treebest best, to redefine the PhyML variable
+ MIN_DIFF_LK
+5) -X option in treebest best, to give a higher weight to the
+ likelihood that comes from the reconciliation with the species tree
+ (default 1)
6) -I option in treebest best, to start from the input tree instead of
building one
7) Species-intersection scores are now also reported as floating-point